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- PDB-1dqh: CRYSTAL STRUCTURE OF HELIX II OF THE X. LAEVIS SOMATIC 5S RRNA WI... -

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Basic information

Entry
Database: PDB / ID: 1dqh
TitleCRYSTAL STRUCTURE OF HELIX II OF THE X. LAEVIS SOMATIC 5S RRNA WITH A CYTOSINE BULGE IN TWO CONFORMATIONS
Components
  • RNA (5'-R(*CP*AP*GP*GP*GP*UP*CP*GP*GP*C)-3')
  • RNA (5'-R(*GP*CP*CP*AP*CP*CP*CP*UP*G)-3')
KeywordsRNA / DOUBLE HELIX / CYTOSINE BULGE
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsXiong, Y. / Sundaralingam, M.
CitationJournal: RNA / Year: 2000
Title: Two crystal forms of helix II of Xenopus laevis 5S rRNA with a cytosine bulge.
Authors: Xiong, Y. / Sundaralingam, M.
History
DepositionJan 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 25, 2012Group: Other
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*GP*CP*CP*AP*CP*CP*CP*UP*G)-3')
B: RNA (5'-R(*CP*AP*GP*GP*GP*UP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,0392
Polymers6,0392
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.78, 32.78, 102.5
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: RNA chain RNA (5'-R(*GP*CP*CP*AP*CP*CP*CP*UP*G)-3')


Mass: 2806.735 Da / Num. of mol.: 1 / Fragment: HELIX II OF 5S RRNA / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(*CP*AP*GP*GP*GP*UP*CP*GP*GP*C)-3')


Mass: 3231.988 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MGCL2, CACL2, CACODYLATE, MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MGCL211
2CACL211
3CACODYLATE11
4MPD11
5MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 mMprotein1drop
20.6 mM1dropMgCl2
34.4 %(v/v)MPD1drop
420.2 mMsodium cacodylate1drop
54.4 mM1dropCaCl2
650 %MPD1reservoir

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Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→22.59 Å / Num. all: 6696 / Num. obs: 6070 / % possible obs: 90.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 20.2

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 653 10.8 %RANDOM
Rwork0.202 ---
obs0.202 6022 90.6 %-
all-6645 --
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 399 0 57 456
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 10.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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